The program tblastn has been modified so that its substitution[unreadable] matrix may be modified by either compositional scaling or conditional[unreadable] compositional matrix adjustment. Because the query is a DNA sequence[unreadable] that is conceptually is translated in six frames, at least five of[unreadable] which are usually incorrect, matrix modification requires the[unreadable] definition of a sequence window from which to calculate sequence[unreadable] composition. We have constructed a way to define such a window[unreadable] that yields good empirical results. Our studies have shown that[unreadable] either type of substitution matrix modification yields statistics[unreadable] that are much more accurate than those of the baseline program,[unreadable] with only a minor attendant decrease in retrieval accuracy.[unreadable] [unreadable] Further work this year has focussed on extending PSI-BLAST so[unreadable] that it is able to use information on correlated sequence positions[unreadable] deduced from multiple alignments.